Navigating Files and Directories
Last updated on 2024-11-14 | Edit this page
Overview
Questions
- How can I perform operations on files outside of my working directory?
- What are some navigational shortcuts I can use to make my work more efficient?
Objectives
- Use a single command to navigate multiple steps in your directory structure, including moving backwards (one level up).
- Perform operations on files in directories outside your working directory.
- Work with hidden directories and hidden files.
- Interconvert between absolute and relative paths.
- Employ navigational shortcuts to move around your file system.
Moving around the file system
We’ve learned how to use pwd
to find our current
location within our file system. We’ve also learned how to use
cd
to change locations and ls
to list the
contents of a directory. Now we’re going to learn some additional
commands for moving around within our file system.
Use the commands we’ve learned so far to navigate to the
shell_data/untrimmed_fastq
directory, if you’re not already
there.
What if we want to move back up and out of this directory and to our
top level directory? Can we type cd shell_data
? Try it and
see what happens.
OUTPUT
-bash: cd: shell_data: No such file or directory
Your computer looked for a directory or file called
shell_data
within the directory you were already in. It
didn’t know you wanted to look at a directory level above the one you
were located in.
We have a special command to tell the computer to move us back or up one directory level.
Now we can use pwd
to make sure that we are in the
directory we intended to navigate to, and ls
to check that
the contents of the directory are correct.
OUTPUT
/home/<username>/obss_2024/commandline/shell_data
OUTPUT
sra_metadata untrimmed_fastq
From this output, we can see that ..
did indeed take us
back one level in our file system.
You can chain these together like so:
prints the contents of
/home/<username>/obss_2024
.
First use the man
command to look at the options for
ls
.
The -a
option is short for all
and says
that it causes ls
to “not ignore entries starting with .”
This is the option we want.
OUTPUT
. .. .hidden sra_metadata untrimmed_fastq
The name of the hidden directory is .hidden
. We can
navigate to that directory using cd
.
And then list the contents of the directory using
ls
.
OUTPUT
youfoundit.txt
The name of the text file is youfoundit.txt
.
In most commands the flags can be combined together in no particular order to obtain the desired results/output.
$ ls -Fa
$ ls -laF
Examining the contents of other directories
By default, the ls
commands lists the contents of the
working directory (i.e. the directory you are in). You can always find
the directory you are in using the pwd
command. However,
you can also give ls
the names of other directories to
view. Navigate to your home directory if you are not already there.
Then enter the command:
OUTPUT
sra_metadata untrimmed_fastq
This will list the contents of the shell_data
directory
without you needing to navigate there.
The cd
command works in a similar way.
Try entering:
This will take you to the untrimmed_fastq
directory
without having to go through the intermediate directory.
Full vs. Relative Paths
The cd
command takes an argument which is a directory
name. Directories can be specified using either a relative path
or a full absolute path. The directories on the computer are
arranged into a hierarchy. The full path tells you where a directory is
in that hierarchy. Navigate to the home directory, then enter the
pwd
command.
You will see:
OUTPUT
/home/<username>
This is the full name of your home directory. This tells you that you
are in a directory called dcuser
, which sits inside a
directory called home
which sits inside the very top
directory in the hierarchy. The very top of the hierarchy is a directory
called /
which is usually referred to as the root
directory. So, to summarize: dcuser
is a directory in
home
which is a directory in /
. More on
root
and home
in the next section.
Now enter the following command:
This jumps forward multiple levels to the .hidden
directory. Now go back to the home directory.
You can also navigate to the .hidden
directory
using:
These two commands have the same effect, they both take us to the
.hidden
directory. The first uses the absolute path, giving
the full address from the home directory. The second uses a relative
path, giving only the address from the working directory. A full path
always starts with a /
. A relative path does not.
A relative path is like getting directions from someone on the street. They tell you to “go right at the stop sign, and then turn left on Main Street”. That works great if you’re standing there together, but not so well if you’re trying to tell someone how to get there from another country. A full path is like GPS coordinates. It tells you exactly where something is no matter where you are right now.
You can usually use either a full path or a relative path depending on what is most convenient. If we are in the home directory, it is more convenient to enter the full path. If we are in the working directory, it is more convenient to enter the relative path since it involves less typing.
Over time, it will become easier for you to keep a mental note of the structure of the directories that you are using and how to quickly navigate amongst them.
Relative path resolution
Using the filesystem diagram below, if pwd
displays
/Users/thing
, what will ls ../backup
display?
../backup: No such file or directory
2012-12-01 2013-01-08 2013-01-27
2012-12-01/ 2013-01-08/ 2013-01-27/
original pnas_final pnas_sub
- No: there is a directory
backup
in/Users
. - No: this is the content of
Users/thing/backup
, but with..
we asked for one level further up. - No: see previous explanation. Also, we did not specify
-F
to display/
at the end of the directory names. - Yes:
../backup
refers to/Users/backup
.
Navigational Shortcuts
The root directory is the highest level directory in your file system
and contains files that are important for your computer to perform its
daily work. While you will be using the root (/
) at the
beginning of your absolute paths, it is important that you avoid working
with data in these higher-level directories, as your commands can
permanently alter files that the operating system needs to function. In
many cases, trying to run commands in root
directories will
require special permissions which are not discussed here, so it’s best
to avoid them and work within your home directory. Dealing with the
home
directory is very common. The tilde character,
~
, is a shortcut for your home directory. In our case, the
root
directory is two levels above our
home
directory, so cd
or cd ~
will take you to /home/<username>
and
cd /
will take you to /
. Navigate to the
shell_data
directory:
Then enter the command:
OUTPUT
obss_2024
This prints the contents of your home directory, without you needing to type the full path.
The commands cd
, and cd ~
are very useful
for quickly navigating back to your home directory. We will be using the
~
character in later lessons to specify our home
directory.
Key Points
- The
/
,~
, and..
characters represent important navigational shortcuts. - Hidden files and directories start with
.
and can be viewed usingls -a
. - Relative paths specify a location starting from the current location, while absolute paths specify a location from the root of the file system.